pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids
Class Aminoacid

java.lang.Object
  pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

Direct Known Subclasses:

Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, Valine

public abstract class Aminoacid
extends java.lang.Object

A skeleton for building every concrete aminoacid. Declaring as abstract prevents from strange side effects (generic aacid is not needed in this context).

See Also:

AminoacidProperties

Field Summary

protected float	absdeviation avergage dihedral angle between two consecutive peptide bond planes (taken twice)
protected float	avgdihedralangle avergage dihedral angle between two consecutive peptide bond planes (taken twice)
protected Atom	C Carbon from {carbonyl group at Calpha}
protected Atom	Ca Carbon alpha
protected float	deviation avergage dihedral angle between two consecutive peptide bond planes (taken twice)
protected float	lnradiusofcurvature radius of curvature of the pentapeptide in which this aacid is the central one
protected Atom	N Nitrogen from amid group at Calpha
protected Atom	O Oxygen from {carbonyl group at Calpha}
protected java.lang.String	pdbindex Sequential residue number, must be String because of so called iColde.
protected float	phi backbone phi torsional angle
protected float	psi backbone psi torsional angle

Constructor Summary

Aminoacid(java.lang.String residuepdbcode, java.util.Map AtomCoords)
Creates a new instance of the Cysteine aminoacid.

Method Summary

abstract java.lang.String	getAbbrev()
float	getAbsDeviation()
float	getAvgDihedralAngle()
java.util.List	getBackboneAtoms()
java.util.List<Atom>	getBackboneAtomsWithoutOcarbonyl()
java.util.List<Bond>	getBackboneBonds()
Atom	getCcarbonyl()
float[]	getCoordsOfCalpha()
float[]	getCoordsOfCcarbonyl()
float[]	getCoordsOfNamid()
float[]	getCoordsOfOcarbonyl()
float	getDeviation()
float	getLnRadiusOfCurvature()
Atom	getNamid()
float	getPhiAngle()
float	getPsiAngle()
java.lang.String	getResiduePdbIndex()
void	setAbsDeviation(float absd)
void	setAvgDihedralAngle(float avgdh) sets average dihedral angle between two consecutive bond planes and between the pair of planes just one aacid next to
void	setDeviation(float d)
void	setLnRadiusOfCurvature(float lnr) sets radius of curvature of the pentapeptide in which current aminoacid is the central one
void	setPhiAngle(Atom prevC) Calls calcTorsionalAngle with appropriate atoms.
void	setPsiAngle(Atom nextN) Calls calcTorsionalAngle with appropriate atoms.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

pdbindex

protected java.lang.String pdbindex

Sequential residue number, must be String because of so called iColde. For more info see Pdb Format Guide, section ATOM.

N

protected Atom N

Nitrogen from amid group at C_alpha

Ca

protected Atom Ca

Carbon _alpha

C

protected Atom C

Carbon from {carbonyl group at C_alpha}

O

protected Atom O

Oxygen from {carbonyl group at C_alpha}

phi

protected float phi

backbone phi torsional angle

psi

protected float psi

backbone psi torsional angle

lnradiusofcurvature

protected float lnradiusofcurvature

radius of curvature of the pentapeptide in which this aacid is the central one

avgdihedralangle

protected float avgdihedralangle

avergage dihedral angle between two consecutive peptide bond planes (taken twice)

deviation

protected float deviation

avergage dihedral angle between two consecutive peptide bond planes (taken twice)

absdeviation

protected float absdeviation

avergage dihedral angle between two consecutive peptide bond planes (taken twice)

Constructor Detail

Aminoacid

public Aminoacid(java.lang.String residuepdbcode,
                 java.util.Map AtomCoords)

Creates a new instance of the Cysteine aminoacid.

Parameters:

residuepdbcode - sequential residue number due to PDB file

AtomCoords - a HashMap with atom coordinates

Method Detail

getAbbrev

public abstract java.lang.String getAbbrev()

Returns:

three-letter abbreviation for the kind of aminoacid

getCoordsOfNamid

public float[] getCoordsOfNamid()

Returns:

coordinates of a Nitrogen from {amid group at C_alpha}

getCoordsOfCalpha

public float[] getCoordsOfCalpha()

Returns:

coordinates of a C_alpha

getCoordsOfCcarbonyl

public float[] getCoordsOfCcarbonyl()

Returns:

coordinates of a Carbon from {carbonyl group at C_alpha}

getCoordsOfOcarbonyl

public float[] getCoordsOfOcarbonyl()

Returns:

coordinates of an Oxygen at Carbon in {carbonyl group at C_alpha}

getResiduePdbIndex

public java.lang.String getResiduePdbIndex()

Returns:

sequential number of an aminoacid in a peptide chain (sometimes with iCode)

getBackboneAtoms

public java.util.List getBackboneAtoms()

Returns:

list of backbone atoms

getBackboneAtomsWithoutOcarbonyl

public java.util.List<Atom> getBackboneAtomsWithoutOcarbonyl()

Returns:

list of backbone atoms without O from carbonyl group at C_alpha. For drawing purposes.

getBackboneBonds

public java.util.List<Bond> getBackboneBonds()

Returns:

list of backbone covalent bonds within single aminoacid (e.i. NOT PEPTIDE BONDS)

getNamid

public Atom getNamid()

Returns:

nitrogen atom from the amid group bound to every C_alpha

getCcarbonyl

public Atom getCcarbonyl()

Returns:

carbon atom from the carbonyl group bound to every C_alpha

setPhiAngle

public void setPhiAngle(Atom prevC)

Calls calcTorsionalAngle with appropriate atoms.

Parameters:

prevC - carbon atom from a previous aminoacid in the chain

See Also:

Math3d.calcTorsionalAngle(pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3, pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3, pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3, pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3)

setPsiAngle

public void setPsiAngle(Atom nextN)

Calls calcTorsionalAngle with appropriate atoms.

Parameters:

nextN - nitrogen atom from a next aminoacid in the chain

See Also:

Math3d.calcTorsionalAngle(pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3, pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3, pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3, pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3)

getPhiAngle

public float getPhiAngle()

Returns:

phi torsional angle for the aminoacid

getPsiAngle

public float getPsiAngle()

Returns:

psi torsional angle for the aminoacid

getLnRadiusOfCurvature

public float getLnRadiusOfCurvature()

Returns:

radius of curvature of the pentapeptide in which the current aminoacid is the central one

setLnRadiusOfCurvature

public void setLnRadiusOfCurvature(float lnr)

sets radius of curvature of the pentapeptide in which current aminoacid is the central one

Parameters:

lnr - natural logarithm o the radius of curvature to be assigned

getAvgDihedralAngle

public float getAvgDihedralAngle()

Returns:

average dihedral angle between two consecutive bond planes and between the pair of planes just one aacid next to

setAvgDihedralAngle

public void setAvgDihedralAngle(float avgdh)

sets average dihedral angle between two consecutive bond planes and between the pair of planes just one aacid next to

Parameters:

avgdh - dihedral angle to be assigned

setDeviation

public void setDeviation(float d)

setAbsDeviation

public void setAbsDeviation(float absd)

getDeviation

public float getDeviation()

getAbsDeviation

public float getAbsDeviation()